recipe bioconductor-amplican

Automated analysis of CRISPR experiments

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/amplican.html

License:

GPL-3

Recipe:

/bioconductor-amplican/meta.yaml

`amplican` performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.

package bioconductor-amplican

Versions:

1.20.0-0,  1.16.0-2,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0,  1.10.0-0,  1.8.0-0, 

1.20.0-0,  1.16.0-2,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0,  1.10.0-0,  1.8.0-0,  1.6.2-0,  1.4.0-0

Depends:

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-biocparallel >=1.32.0,<1.33.0

• bioconductor-biostrings >=2.66.0,<2.67.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-shortread >=1.56.0,<1.57.0

• libblas >=3.9.0,<4.0a0

• libgcc-ng >=12

• liblapack >=3.9.0,<4.0a0

• libstdcxx-ng >=12

• r-base >=4.2,<4.3.0a0

• r-clustercrit >=1.2.7

• r-data.table >=1.10.4-3

• r-dplyr >=0.7.2

• r-ggplot2 >=2.2.0

• r-ggthemes >=3.4.0

• r-gridextra >=2.2.1

• r-gtable >=0.2.0

• r-knitr >=1.16

• r-matrix >=1.2-10

• r-matrixstats >=0.52.2

• r-rcpp

• r-rmarkdown >=1.6

• r-stringr >=1.2.0

• r-waffle >=0.7.0

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-amplican

and update with:

conda update bioconductor-amplican

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-amplican:<tag>

(see bioconductor-amplican/tags for valid values for <tag>)

Download stats

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-amplican/README.html)